As a consequence of the treaty, Warmia became an autonomous region ruled by bishop of Warmia (see Duchy of Warmia). Eastern Prussia, later called Duchy of Prussia remained with the Teutonic Order until 1525 and the grandmaster was supposed to swear a personal oath (the Prussian homage) to the king of Poland and to furnish him with military. In order to avoid giving the oath, the new Grand Masters made it simply their practice not to visit Prussia.

The treaty stated that Royal Prussia became the exclusive property of Polish king and Polish kingdom. Later some disagreements arose concerning certain prerogatives that Royal Prussia and the cities held, like Danzig's privileges. While the Polish side considered it simply part of the kingdom, Royal Prussians insisted on and defended their guaranteed autonomy. The government differed from the Polish kingdom, they had privileges such as the minting of its own coins, its own Diet meetings (see the Prussian estates), its own military, and its own administrative usage of the German language. Prussians were denied the right to name bishops in Royal Prussia and decided not to take the seats provided for them in the Sejm. This conflict eventually led to the War of the Priests (1467–79). Eventually, Royal Prussia would become increasingly integrated into the Polish-Lithuanian Commonwealth, but would retain some distinctive features until the partitions of Poland in the late 18th century.